On 10/15/12 1:03 PM, Amir Abbasi wrote:
tnx But I need these two planes angle too.
what should I do?
can I convert all of trajectory file to pdb?
in order to do these manually?
That would be extremely inefficient. Determining what's wrong with your index
file is probably a much better solution.
-Justin
--------------------------------------------------------------------------------
*From:* Justin Lemkul <jalem...@vt.edu>
*To:* Amir Abbasi <amir.abbas...@yahoo.com>; Discussion list for GROMACS users
<gmx-users@gromacs.org>
*Sent:* Monday, October 15, 2012 7:47 PM
*Subject:* Re: [gmx-users] no groups in indexfile!
On 10/15/12 11:48 AM, Amir Abbasi wrote:
> Hi !
> I want to use g_sgangle to find distance between two groups (each group
includes 3 atoms).
> I use this command:
> g_sgangle -s md_1.tpr -f md_1_noPBC.xtc -n index.ndx -oa 12_angle.xvg -od
12_dist.xvg
> but i got this error
> Fatal error:
> Error: no groups in indexfile
>
> my index file:
> [ G3 ]
> 76 81 85
> [ G4 ]
> 110 115 119
>
The most likely explanation is that you have some problem with non-Unix line
endings in the file. Note that if you just need distances between groups,
g_dist is more efficient for that calculation.
-Justin
-- ========================================
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
--
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